Fragmentation patterns of protonated amino acids formed by atmospheric pressure chemical ionization.

Rationale: Dissociation reactions of protonated amino acids (AAs) can be used as models for the fragmentation of protonated peptides. Atmospheric pressure chemical ionization mass spectrometry (APCI-MS) provides a great deal of structural information in a short analysis time.

Methods: In APCI-MS, the fragmentation patterns can be obtained by varying the cone voltage and some fragment ions are produced that can be used to identify the structure of an analyte. In general, the fragmentation of AAs has used liquid chromatography/tandem mass spectrometry (LC/MS/MS). However, we studied the fragmentation of protonated AAs using a single quadrupole mass spectrometer.

Results: The principal fragment ions were [M + H - H(2)O - CO](+), [M + H - H(2)O](+), and [M + H - NH(3)](+). AAs that only generated [M + H - H(2)O - CO](+) were alanine, glycine, histidine, isoleucine, leucine, proline, phenylalanine, and valine. AAs that generated [M + H - H(2)O](+) and [M + H - H(2)O - CO](+) were aspartic acid, glutamic acid, serine, and threonine, while AAs that generated [M + H - NH(3)](+) and [M + H - H(2)O - CO](+) were asparagine, cysteine, glutamine, methionine, tryptophan, and tyrosine. Arginine and lysine generated [M + H - H(2)O](+) and [M + H - NH(3)](+).

Conclusions: The relative abundances of the fragment ions increased with increase in the cone voltage. The experimental results were explained by the favorability of the intermediate structure and the stability of the fragment ion structure. The specific fragmentation patterns could be used for differentiating underivatized AAs.